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Source Code for Biology and Medicine

ISSN Print: 1751-0473

ISSN Online:

Website: http://www.scfbm.org

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BlaSTorage: a fast package to parse, manage and store BLAST results

Orsini Massimiliano,Carcangiu Simone

Changing computational research. The challenges ahead

Cameron Neylon, Jan Aerts, C Titus Brown, Daniel Lemire, Jarrod Millman, Peter Murray-Rust, Fernando Perez, Neil Saunders, Arfon Smith, Ga？l Varoquaux, Egon Willighagen

How Not to Be a Bioinformatician

Manuel Corpas, Segun Fatumo, Reinard Schneider

Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments

Ricardo H Ramirez-Gonzalez, Raoul Bonnal, Mario Caccamo, Daniel MacLean

Scaffolder - software for manual genome scaffolding

Michael D Barton, Hazel A Barton

Automatic Fortran to C++ conversion with FABLE

Ralf W Grosse-Kunstleve, Thomas C Terwilliger, Nicholas K Sauter, Paul D Adams

Yabi: An online research environment for grid, high performance and cloud computing

Adam A Hunter, Andrew B Macgregor, Tamas O Szabo, Crispin A Wellington, Matthew I Bellgard

Layout-aware text extraction from full-text PDF of scientific articles

Cartic Ramakrishnan, Abhishek Patnia, Eduard Hovy, Gully APC Burns

JobCenter: an open source, cross-platform, and distributed job queue management system optimized for scalability and versatility

Jaschob Daniel,Riffle Michael

CADLIVE optimizer: web-based parameter estimation for dynamic models

Inoue Kentaro,Maeda Kazuhiro,Kato Yuki,Tonami Shinpei

PathNet: a tool for pathway analysis using topological information

Dutta Bhaskar,Wallqvist Anders,Reifman Jaques

WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results

Vineet K Joshi, Johannes M Freudenberg, Zhen Hu, Mario Medvedovic

Tools for efficient epistasis detection in genome-wide association study

Xiang Zhang, Shunping Huang, Fei Zou, Wei Wang

Parallel biocomputing

Kenneth S Kompass, Thomas J Hoffmann, John S Witte

Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format

Ryan L Webb, Avi Ma'ayan

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format

Guorong Xu, Nan Deng, Zhiyu Zhao, Thair Judeh, Erik Flemington, Dongxiao Zhu

Creating web applications for spatial epidemiological analysis and mapping in R using Rwui

Richard Newton, Andrew Deonarine, Lorenz Wernisch

KBWS: an EMBOSS associated package for accessing bioinformatics web services

Kazuki Oshita, Kazuharu Arakawa, Masaru Tomita

WordCloud: a Cytoscape plugin to create a visual semantic summary of networks

Layla Oesper, Daniele Merico, Ruth Isserlin, Gary D Bader

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text

Caroline Baroukh, Sherry L Jenkins, Ruth Dannenfelser, Avi Ma'ayan

SNIT: SNP identification for strain typing

Ravi Vijaya Satya, Nela Zavaljevski, Jaques Reifman

A proof of the DBRF-MEGN method, an algorithm for deducing minimum equivalent gene networks

Koji Kyoda, Kotaro Baba, Hiroaki Kitano, Shuichi Onami

Nephele: genotyping via complete composition vectors and MapReduce

Marc E Colosimo, Matthew W Peterson, Scott Mardis, Lynette Hirschman

LimsPortal and BonsaiLIMS: development of a lab information management system for translational medicine

Timothy G Bath, Selcuk Bozdag, Vackar Afzal, Daniel Crowther

ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing

Kazuharu Misawa, Naoyuki Kamatani

CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes

Marco Galardini, Emanuele G Biondi, Marco Bazzicalupo, Alessio Mengoni

Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information

Chandra Sekhar Pedamallu, Janos Posfai

EntrezAJAX: direct web browser access to the Entrez Programming Utilities

Nicholas J Loman, Mark J Pallen

GTC: A web server for integrating systems biology data with web tools and desktop applications

Dan Tenenbaum, J Christopher Bare, Nitin S Baliga

ParaHaplo 2.0: a program package for haplotype-estimation and haplotype-based whole-genome association study using parallel computing

Kazuharu Misawa, Naoyuki Kamatani

Dockres: a computer program that analyzes the output of virtual screening of small molecules

Mihaly Mezei, Ming-Ming Zhou

VersaCount: customizable manual tally software for cell counting

Charles C Kim, Joseph L DeRisi

DOG-SPOT database for comprehensive management of dog genetic research data

Julie AS Powell, Jeremy Allen, Nathan B Sutter

IHE cross-enterprise document sharing for imaging: interoperability testing software

Rita Noumeir, Bérubé Renaud

A methodology for projecting hospital bed need: a Michigan case study

Shaun A Langley, Steven P Fuller, Joseph P Messina, Ashton M Shortridge, Sue C Grady

MADAM - An open source meta-analysis toolbox for R and Bioconductor

Karl G Kugler, Laurin AJ Mueller, Armin Graber

Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format

Justina Krawczyk, Alexander Goesmann, Ralf Nolte, Martin Werber, Bernd Weisshaar

HAMSTER: visualizing microarray experiments as a set of minimum spanning trees

Raymond Wan, Larisa Kiseleva, Hajime Harada, Hiroshi Mamitsuka, Paul Horton

A web server for interactive and zoomable Chaos Game Representation images

Kazuharu Arakawa, Kazuki Oshita, Masaru Tomita

Motmot, an open-source toolkit for realtime video acquisition and analysis

Andrew D Straw, Michael H Dickinson

GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction

Fiona Browne, Haiying Wang, Huiru Zheng, Francisco Azuaje

KinImmerse: Macromolecular VR for NMR ensembles

Jeremy N Block, David J Zielinski, Vincent B Chen, Ian W Davis, E Claire Vinson, Rachael Brady, Jane S Richardson, David C Richardson

A software pipeline for processing and identification of fungal ITS sequences

R Henrik Nilsson, Gunilla Bok, Martin Ryberg, Erik Kristiansson, Nils Hallenberg

ParaHaplo: A program package for haplotype-based whole-genome association study using parallel computing

Kazuharu Misawa, Naoyuki Kamatani

Boolean network simulations for life scientists

István Albert, Juilee Thakar, Song Li, Ranran Zhang, Réka Albert

Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data

Nicolas J Parker, Andrew G Parker

Wndchrm – an open source utility for biological image analysis

Lior Shamir, Nikita Orlov, D Mark Eckley, Tomasz Macura, Josiah Johnston, Ilya G Goldberg

CRANKITE: A fast polypeptide backbone conformation sampler

Alexei A Podtelezhnikov, David L Wild

Purposeful selection of variables in logistic regression

Zoran Bursac, C Heath Gauss, David Keith Williams, David W Hosmer

A Perl toolkit for LIMS development

James A Morris, Simon A Gayther, Ian J Jacobs, Christopher Jones

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